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    <title>PDEXK recognition Web Server: Help</title>
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            PDEXK recognition server HELP
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        PDEXK recognition is a method for detecting new protein families of PDEXK clan using Support Vector Machines. 
        Short description of server input options and output is given below.<br/>
        <br/>
        
        <div class="title">
            <a name="server_input">
               Server input
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		<!--Input-->
		<a name="input" class="group">
		Input
		</a><br/><br/>
		
		<a name="paste_sequence" class="anchor">
		Paste protein sequence or multiple alignment
		</a><br/>
		<span class="description">
		Paste a single protein sequence or multiple alignment in the format defined by the 'Input type'.
		Currently, only the FASTA format is accepted. If a multiple sequence alignment is provided, 
		the length of aligned sequences must be the same.
		</span><br/><br/>
		
		<!--Upload a local file-->
		<a name="upload_local" class="anchor">
		Upload a local file
		</a><br/>
		<span class="description">
		Optionally, user may upload a local file containing a single protein sequence or multiple sequence alignment in the format defined by the 'Input type'.
		</span><br/><br/>
		
		<!--Input type-->
		<a name="input_type" class="anchor">
		Input type
		</a><br/>
		<span class="description">
		Describes the format of input protein sequence(s). Currently, The FASTA format is available. Each sequence in this format has a description line starting with symbol '>', e.g.:<br/>
		>3i1m_R mol:protein length:75  30S ribosomal protein S18<br/>
		MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ
		</span><br/><br/>
		
		<!--E-mail results to-->
		<a name="email_results_to" class="anchor">
		E-mail results to
		</a><br/>
		<span class="description">
		Once the job is finished, the results will be sent to the E-mail address provided in this field. It is strongly recommended to provide E-mail address, as the E-mail message contains the link to the results of the finished job. 
		</span><br/><br/>
		
		<!--Job description (max 20 characters)-->
		<a name="job_description" class="anchor">
		Job description (max 20 characters)
		</a><br/>
		<span class="description">
		A user may provide an optional job identifier of maximum length of 20 characters.
		</span><br/><br/>
		
		<!--Construction of query-based multiple alignment using PSI-BLAS-->
        <a name="construction_msa" class="group">
        Construction of multiple sequence alignment using PSI-BLAST
        </a><br/><br/>
        
        <!--Do not run PSI-BLAST (use my input multiple alignment)-->
        <a name="do_not_run_psiblast" class="anchor">
        Do not run PSI-BLAST (use my input multiple alignment)
        </a><br/>
        <span class="description">
        Providing a custom multiple sequence alignment as an input and checking this option disallows PSI-BLAST run using the provided multiple sequence alignment for jumpstart; the input alignment is used directly to construct query profile.      </span><br/><br/>
        
        <!--Let the server handle PSI-BLAST run-->
        <a name="let_the_server_handle" class="anchor">
        Let the server handle PSI-BLAST run
        </a><br/>
        <span class="description">
        Selecting this option means that the server will take control of the process of profile construction.     </span><br/><br/>
		
		<div class="title">
			<a name="server_output">
	           Server output
	        </a>
		</div>
        
        <a name="input_seq" class="anchor">
        Sequence or MSA
        </a><br/>
        <span class="description">
        A file that contains an input sequence or an input multiple sequence alignment.     </span><br/><br/>
        
        <a name="input_par" class="anchor">
        Parameters
        </a><br/>
        <span class="description">
        A file that contains an input parameters for the server run.     </span><br/><br/>
        
        <a name="output_logs" class="anchor">
        STDERR log, STDOUT log 
        </a><br/>
        <span class="description">
        The files that contain logging information (stdout and stderr).     </span><br/><br/>
 
        <a name="fma" class="anchor">
        Final multiple alignment 
        </a><br/>
        <span class="description">
        A constructed final multiple alignment if PSI-BlAST was used. Otherwise only secondary structure information is added to the input multiple sequence alignment.     </span><br/><br/>

        <a name="comparison_of_msa" class="anchor">
        Comparison of MSA 
        </a><br/>
        <span class="description">
        A <a href="http://toolkit.tuebingen.mpg.de/hhpred/help_results">HHsearch</a> output file.     </span><br/><br/>

        <a name="aligned_pdexk" class="anchor">
        Aligned PDEXK  
        </a><br/>
        <span class="description">
        A pseudo multiple sequence alignment with the following structure:
        <ol>
		  <li>>ss_pred - a secondary structure sequence predicted with <a href="http://www.psipred.net/psiform.html">PSI-PRED</a></li>
		  <li>>Consensus - a consensus sequence given by <a href="http://toolkit.tuebingen.mpg.de/hhpred/help_results">HHsearch</a></li>
		  <li>>A1W682_ACISJ/1 - a query sequence (or the first sequence in the given MSA)</li>
		  <li>>DELIM1 - a delimiter line</li>
		  <li>>PDEXK_family_pdexk - a line that defines conservative positions of the PDEXK_family. 1 - E position; 2 - PD; 3 - EXK.</li>
		  <li>>PDEXK_family - the PDEXK protein family that was aligned with the query using <a href="http://toolkit.tuebingen.mpg.de/hhpred/help_results">HHsearch</a></li>
		  <li>>DELIM2 - a delimiter line</li>
		  <li>Final multiple alignment</li>
        </ol>
        </span>

        <a name="svm_probability" class="anchor">
        SVM Probability  
        </a><br/>
        <span class="description">
        A file that contains SVM prediction probabilities given by SVM classifiers.
        The file structure is the following: classifier name, its training accuracy and predicted probability.</span><br/><br/>
        
        <a name="predicted_probability" class="anchor">
        Predicted probability   
        </a><br/>
        <span class="description">
	        <div style="width: 600px; height: auto;  margin: 5px; padding: 5px; color: white; background-color: green;">
	             <b>[0.7, 1.0]. A query protein family is considered as a member of PDEXK clan.</b>
	        </div>
	        <div style="width: 600px; height: auto; margin: 5px; padding: 5px; color: white; background-color: blue;">
		         <b>[0.5, 0.7). Uncertain.</b>
		    </div><div style="width: 600px; height: auto; margin: 5px; padding: 5px; color: white; background-color: red;">
	             <b>[0.0, 0.5). Unlikely. -1 means that no PDEXK was aligned with the query.</b>
	        </div>
        </span><br/>
        
        <div class="title">
            <a name="server_output">
               References
            </a>
        </div>
        <span class="description">
            <ol>
                <li>
                    Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. JMB 292: 195-202.
                </li>
                <li>        
                    Lin, H.-T.and Li, L. (2008) Support vector machinery for infinite ensemble learning. J. Mach. Learn. Res., 9, 285-312.
                </li>
                <li>        
                    Söding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
                </li>
            </ol>
        </span>
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